PDEL_ECOLI
ID PDEL_ECOLI Reviewed; 362 AA.
AC P21514; P75689; Q2MCA8;
DT 01-MAY-1991, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 2.
DT 03-AUG-2022, entry version 159.
DE RecName: Full=Cyclic di-GMP phosphodiesterase PdeL {ECO:0000305};
DE EC=3.1.4.52 {ECO:0000269|PubMed:15995192, ECO:0000269|PubMed:24451384, ECO:0000269|PubMed:26553851};
GN Name=pdeL {ECO:0000303|PubMed:26148715}; Synonyms=yahA;
GN OrderedLocusNames=b0315, JW0307;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RA Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M.,
RA Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D.,
RA Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.;
RT "Sequence of minutes 4-25 of Escherichia coli.";
RL Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-126.
RC STRAIN=K12;
RX PubMed=1956285; DOI=10.1111/j.1365-2958.1991.tb01877.x;
RA Lamark T., Kaasen E., Eshoo M.W., Falkenberg P., McDougall J., Strom A.R.;
RT "DNA sequence and analysis of the bet genes encoding the osmoregulatory
RT choline-glycine betaine pathway of Escherichia coli.";
RL Mol. Microbiol. 5:1049-1064(1991).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ACTIVITY REGULATION, AND
RP BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=15995192; DOI=10.1128/jb.187.14.4774-4781.2005;
RA Schmidt A.J., Ryjenkov D.A., Gomelsky M.;
RT "The ubiquitous protein domain EAL is a cyclic diguanylate-specific
RT phosphodiesterase: enzymatically active and inactive EAL domains.";
RL J. Bacteriol. 187:4774-4781(2005).
RN [6]
RP NOMENCLATURE.
RX PubMed=26148715; DOI=10.1128/jb.00424-15;
RA Hengge R., Galperin M.Y., Ghigo J.M., Gomelsky M., Green J., Hughes K.T.,
RA Jenal U., Landini P.;
RT "Systematic nomenclature for GGDEF and EAL domain-containing cyclic di-GMP
RT turnover proteins of Escherichia coli.";
RL J. Bacteriol. 198:7-11(2015).
RN [7]
RP FUNCTION, DNA-BINDING, CATALYTIC ACTIVITY, INDUCTION, AND MUTAGENESIS OF
RP LYS-60; PHE-206; PHE-249 AND GLY-299.
RX PubMed=26553851; DOI=10.1128/jb.00604-15;
RA Reinders A., Hee C.S., Ozaki S., Mazur A., Boehm A., Schirmer T., Jenal U.;
RT "Expression and genetic activation of cyclic di-GMP-specific
RT phosphodiesterases in Escherichia coli.";
RL J. Bacteriol. 198:448-462(2015).
RN [8] {ECO:0007744|PDB:4KIE, ECO:0007744|PDB:4LJ3, ECO:0007744|PDB:4LYK}
RP X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF 96-362 IN COMPLEXES WITH
RP MAGNESIUM; C-DI-GMP AND CALCIUM, FUNCTION, CATALYTIC ACTIVITY, COFACTOR,
RP ACTIVITY REGULATION, SUBUNIT, AND MUTAGENESIS OF ASP-263 AND SER-298.
RX PubMed=24451384; DOI=10.1074/jbc.m113.516195;
RA Sundriyal A., Massa C., Samoray D., Zehender F., Sharpe T., Jenal U.,
RA Schirmer T.;
RT "Inherent regulation of EAL domain-catalyzed hydrolysis of second messenger
RT cyclic di-GMP.";
RL J. Biol. Chem. 289:6978-6990(2014).
CC -!- FUNCTION: Acts both as an enzyme and as a c-di-GMP sensor to couple
CC transcriptional activity to the c-di-GMP status of the cell
CC (PubMed:26553851). Phosphodiesterase (PDE) that catalyzes the
CC hydrolysis of cyclic-di-GMP (c-di-GMP) to 5'-pGpG (PubMed:15995192,
CC PubMed:24451384, PubMed:26553851). Also acts as a transcription factor
CC to control its own expression (PubMed:26553851).
CC {ECO:0000269|PubMed:15995192, ECO:0000269|PubMed:24451384,
CC ECO:0000269|PubMed:26553851}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cyclic di-3',5'-guanylate + H2O = 5'-
CC phosphoguanylyl(3'->5')guanosine + H(+); Xref=Rhea:RHEA:24902,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:58754,
CC ChEBI:CHEBI:58805; EC=3.1.4.52;
CC Evidence={ECO:0000269|PubMed:15995192, ECO:0000269|PubMed:24451384,
CC ECO:0000269|PubMed:26553851};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:15995192, ECO:0000269|PubMed:24451384};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:15995192};
CC -!- ACTIVITY REGULATION: Strongly inhibited by Ca(2+).
CC {ECO:0000269|PubMed:15995192, ECO:0000269|PubMed:24451384}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=25 uM for c-di-GMP {ECO:0000269|PubMed:15995192};
CC pH dependence:
CC Optimum pH is 9.35. {ECO:0000269|PubMed:15995192};
CC -!- SUBUNIT: Is in a fast thermodynamic monomer-homodimer equilibrium.
CC Dimerization is required for PDE activity. Dimerization affinity is
CC increased about 100-fold upon substrate binding.
CC {ECO:0000269|PubMed:24451384}.
CC -!- INDUCTION: Autoregulated. Directly regulates its own expression in a c-
CC di-GMP-dependent manner. {ECO:0000269|PubMed:26553851}.
CC -!- MISCELLANEOUS: An overexpressed EAL domain (residues 77-362) has
CC similar KM, Vmax, pH and metal dependence and subunit composition as
CC the full-length protein. {ECO:0000305|PubMed:15995192}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAB18041.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; U73857; AAB18041.1; ALT_INIT; Genomic_DNA.
DR EMBL; U00096; AAC73418.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76098.1; -; Genomic_DNA.
DR EMBL; X52905; CAA37089.1; -; Genomic_DNA.
DR PIR; C64758; C64758.
DR RefSeq; NP_414849.1; NC_000913.3.
DR RefSeq; WP_001301264.1; NZ_SSZK01000075.1.
DR PDB; 4KIE; X-ray; 1.70 A; A=96-362.
DR PDB; 4LJ3; X-ray; 1.70 A; A/B=101-362.
DR PDB; 4LYK; X-ray; 2.40 A; A/B/C/D=101-362.
DR PDBsum; 4KIE; -.
DR PDBsum; 4LJ3; -.
DR PDBsum; 4LYK; -.
DR AlphaFoldDB; P21514; -.
DR SMR; P21514; -.
DR BioGRID; 4262803; 8.
DR IntAct; P21514; 3.
DR STRING; 511145.b0315; -.
DR jPOST; P21514; -.
DR PaxDb; P21514; -.
DR PRIDE; P21514; -.
DR EnsemblBacteria; AAC73418; AAC73418; b0315.
DR EnsemblBacteria; BAE76098; BAE76098; BAE76098.
DR GeneID; 947459; -.
DR KEGG; ecj:JW0307; -.
DR KEGG; eco:b0315; -.
DR PATRIC; fig|1411691.4.peg.1962; -.
DR EchoBASE; EB1218; -.
DR eggNOG; COG2200; Bacteria.
DR eggNOG; COG2771; Bacteria.
DR HOGENOM; CLU_000445_70_50_6; -.
DR InParanoid; P21514; -.
DR OMA; RIAGHAF; -.
DR PhylomeDB; P21514; -.
DR BioCyc; EcoCyc:EG11236-MON; -.
DR BioCyc; MetaCyc:EG11236-MON; -.
DR SABIO-RK; P21514; -.
DR PRO; PR:P21514; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0071111; F:cyclic-guanylate-specific phosphodiesterase activity; IDA:EcoCyc.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0000976; F:transcription cis-regulatory region binding; IDA:EcoCyc.
DR GO; GO:0045893; P:positive regulation of transcription, DNA-templated; IMP:EcoCyc.
DR CDD; cd01948; EAL; 1.
DR CDD; cd06170; LuxR_C_like; 1.
DR Gene3D; 1.10.10.10; -; 1.
DR Gene3D; 3.20.20.450; -; 1.
DR InterPro; IPR001633; EAL_dom.
DR InterPro; IPR035919; EAL_sf.
DR InterPro; IPR016032; Sig_transdc_resp-reg_C-effctor.
DR InterPro; IPR000792; Tscrpt_reg_LuxR_C.
DR InterPro; IPR036388; WH-like_DNA-bd_sf.
DR Pfam; PF00563; EAL; 1.
DR Pfam; PF00196; GerE; 1.
DR SMART; SM00052; EAL; 1.
DR SMART; SM00421; HTH_LUXR; 1.
DR SUPFAM; SSF141868; SSF141868; 1.
DR SUPFAM; SSF46894; SSF46894; 1.
DR PROSITE; PS50883; EAL; 1.
DR PROSITE; PS50043; HTH_LUXR_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; c-di-GMP; DNA-binding; Hydrolase; Magnesium; Manganese;
KW Metal-binding; Reference proteome; Transcription; Transcription regulation.
FT CHAIN 1..362
FT /note="Cyclic di-GMP phosphodiesterase PdeL"
FT /id="PRO_0000168573"
FT DOMAIN 18..83
FT /note="HTH luxR-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00411"
FT DOMAIN 106..360
FT /note="EAL"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00074"
FT DNA_BIND 42..61
FT /note="H-T-H motif"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00411"
FT BINDING 127
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:24451384,
FT ECO:0007744|PDB:4LJ3"
FT BINDING 141
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:24451384,
FT ECO:0007744|PDB:4LYK"
FT BINDING 144..145
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:24451384,
FT ECO:0007744|PDB:4LJ3"
FT BINDING 200
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:24451384,
FT ECO:0007744|PDB:4LYK"
FT BINDING 200
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:24451384,
FT ECO:0007744|PDB:4LJ3"
FT BINDING 232
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:24451384,
FT ECO:0007744|PDB:4LYK"
FT BINDING 262
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:24451384,
FT ECO:0007744|PDB:4LYK"
FT BINDING 262
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:24451384,
FT ECO:0007744|PDB:4LJ3"
FT BINDING 286
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:24451384,
FT ECO:0007744|PDB:4LJ3"
FT BINDING 319..322
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:24451384,
FT ECO:0007744|PDB:4LJ3"
FT BINDING 341
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:24451384,
FT ECO:0007744|PDB:4LJ3"
FT MUTAGEN 60
FT /note="K->A: Does not bind to the PdeL box."
FT /evidence="ECO:0000269|PubMed:26553851"
FT MUTAGEN 206
FT /note="F->S: Increases catalytic activity."
FT /evidence="ECO:0000269|PubMed:26553851"
FT MUTAGEN 249
FT /note="F->L: Increases catalytic activity."
FT /evidence="ECO:0000269|PubMed:26553851"
FT MUTAGEN 263
FT /note="D->N: Loss of activity."
FT /evidence="ECO:0000269|PubMed:24451384"
FT MUTAGEN 298
FT /note="S->W: Slow monomer-dimer exchange. Equilibrium
FT largely on the monomeric side, in particular in the
FT presence of substrate. Strong decrease in activity."
FT /evidence="ECO:0000269|PubMed:24451384"
FT MUTAGEN 299
FT /note="G->S: Increases catalytic activity."
FT /evidence="ECO:0000269|PubMed:26553851"
FT STRAND 105..108
FT /evidence="ECO:0007829|PDB:4LJ3"
FT HELIX 110..118
FT /evidence="ECO:0007829|PDB:4KIE"
FT STRAND 122..131
FT /evidence="ECO:0007829|PDB:4KIE"
FT TURN 132..134
FT /evidence="ECO:0007829|PDB:4LJ3"
FT STRAND 137..148
FT /evidence="ECO:0007829|PDB:4KIE"
FT TURN 149..151
FT /evidence="ECO:0007829|PDB:4KIE"
FT STRAND 152..154
FT /evidence="ECO:0007829|PDB:4KIE"
FT HELIX 156..158
FT /evidence="ECO:0007829|PDB:4KIE"
FT HELIX 160..166
FT /evidence="ECO:0007829|PDB:4KIE"
FT HELIX 169..184
FT /evidence="ECO:0007829|PDB:4KIE"
FT HELIX 185..190
FT /evidence="ECO:0007829|PDB:4KIE"
FT STRAND 195..200
FT /evidence="ECO:0007829|PDB:4KIE"
FT HELIX 203..207
FT /evidence="ECO:0007829|PDB:4KIE"
FT HELIX 211..222
FT /evidence="ECO:0007829|PDB:4KIE"
FT TURN 224..226
FT /evidence="ECO:0007829|PDB:4KIE"
FT STRAND 227..237
FT /evidence="ECO:0007829|PDB:4KIE"
FT HELIX 243..254
FT /evidence="ECO:0007829|PDB:4KIE"
FT STRAND 258..263
FT /evidence="ECO:0007829|PDB:4KIE"
FT HELIX 268..276
FT /evidence="ECO:0007829|PDB:4KIE"
FT STRAND 280..284
FT /evidence="ECO:0007829|PDB:4KIE"
FT HELIX 286..292
FT /evidence="ECO:0007829|PDB:4KIE"
FT HELIX 296..308
FT /evidence="ECO:0007829|PDB:4KIE"
FT TURN 311..313
FT /evidence="ECO:0007829|PDB:4LYK"
FT STRAND 315..318
FT /evidence="ECO:0007829|PDB:4KIE"
FT HELIX 324..332
FT /evidence="ECO:0007829|PDB:4KIE"
FT STRAND 337..340
FT /evidence="ECO:0007829|PDB:4LJ3"
FT TURN 341..343
FT /evidence="ECO:0007829|PDB:4KIE"
FT HELIX 349..356
FT /evidence="ECO:0007829|PDB:4KIE"
SQ SEQUENCE 362 AA; 40725 MW; 4BCA091840F27A0D CRC64;
MNSCDFRVFL QEFGTTVHLS LPGSVSEKER LLLKLLMQGM SVTEISQYRN RSAKTISHQK
KQLFEKLGIQ SDITFWRDIF FQYNPEIISA TGSNSHRYIN DNHYHHIVTP EAISLALENH
EFKPWIQPVF CAQTGVLTGC EVLVRWEHPQ TGIIPPDQFI PLAESSGLIV IMTRQLMKQT
ADILMPVKHL LPDNFHIGIN VSAGCFLAAG FEKECLNLVN KLGNDKIKLV LELTERNPIP
VTPEARAIFD SLHQHNITFA LDDFGTGYAT YRYLQAFPVD FIKIDKSFVQ MASVDEISGH
IVDNIVELAR KPGLSIVAEG VETQEQADLM IGKGVHFLQG YLYSPPVPGN KFISEWVMKA
GG
